Knowledge Enabled Information and Services Science Empowering Translational Research using Semantic Web Technologies OCCBIO, June, 2008 Amit P. Sheth Kno.e.sis Center, Wright State University

Knowledge Enabled Information and Services Science Translational Research & Semantic Web Translate discoveries that typically begin at “the bench” with basic research — in which scientists study disease at a molecular or cellular level — into progress to the clinical level, or the patient's “bedside.” Increasingly biology and biomedical science is a data driven discipline. Dealing with large amounts of distributed and (syntactically, structurally and semantically) heterogeneous data, and analysis of such data is a key challenge. Semantic Web is a Data Web where by associating meaning with data, it is easier to search, integrate and analyze data.

Knowledge Enabled Information and Services Science Translational Medicine... Medical InformaticsBioinformatics Etiology Pathogenesis Clinical findings Diagnosis Prognosis Treatment Genome Transcriptome Proteome Metabolome Physiome...ome Genbank Uniprot PubmedClinical Trials.gov...needs a connection Biomedical Informatics Hypothesis Validation Experiment design Predictions Personalized medicine Semantic Web research aims at providing this connection! More advanced capabilities for search, integration, analysis, linking to new insights and discoveries!

Knowledge Enabled Information and Services Science Evolution of the Web Web of pages - text, manually created links - extensive navigation Web of databases - dynamically generated pages - web query interfaces Web of services - data = service = data, mashups - ubiquitous computing Web of people - social networks, user-created content - GeneRIF, Connotea Web as an oracle / assistant / partner - “ask to the Web” - using semantics to leverage text + data + services + people

Knowledge Enabled Information and Services Science Outline Semantic Web – very brief intro Scenarios to demonstrate the applications Some of the Kno.e.sis capabilities in Semantic Web technologies and their applications to biomedicine and health care in collaboration with biomedical scientists and clinicians

Knowledge Enabled Information and Services Science Ontology: Agreement with Common Vocabulary & Domain Knowledge; Schema + Knowledge base Semantic Annotation (metadata Extraction): Manual, Semi-automatic (automatic with human verification), Automatic Computation/reasoning: disambiguation, semantics enabled search, integration, complex queries, analysis (paths, subgraph), pattern finding, mining, hypothesis validation, discovery, visualization Semantic Web Enablers and Techniques

Knowledge Enabled Information and Services Science Maturing capabilites and ongoing research Text mining: Entity recognition, Relationship extraction Integrating text, experimetal data, curated and multimedia data Clinical and Scientific Workflows with semantic web services Hypothesis driven retrieval of scientific literature, Undiscovered public knowledge

Knowledge Enabled Information and Services Science Opportunity: exploiting clinical and biomedical data text Health Information Services Elsevier iConsult Scientific Literature PubMed 300 Documents Published Online each day User-contributed Content (Informal) GeneRifs NCBI Public Datasets Genome, Protein DBs new sequences daily Laboratory Data Lab tests, RTPCR, Mass spec Clinical Data Personal health history Search, browsing, complex query, integration, workflow, analysis, hypothesis validation, decision support. binary

Knowledge Enabled Information and Services Science Scenario 1: Status: In use today Where: Athens Heart Center What: Use of semantic Web technologies for clinical decision support Also research on adaptive clinical processes

Knowledge Enabled Information and Services Science Operational since January 2006

Knowledge Enabled Information and Services Science Annotate ICD9s Annotate Doctors Lexical Annotation Level 3 Drug Interaction Insurance Formulary Drug Allergy Active Semantic EMR

Knowledge Enabled Information and Services Science Agile Clinical Pathways Volatile nature of execution environments –May have an impact on multiple activities/ tasks in the workflow HF Pathway –New information about diseases, drugs becomes available –Affects treatment plans, drug-drug interactions Need to incorporate the new knowledge into execution –capture the constraints and relationships between different tasks activities

Knowledge Enabled Information and Services Science New knowledge about treatment found during the execution of the pathway New knowledge about drugs, drug drug interactions

Knowledge Enabled Information and Services Science Extraction and Annotation using an ontology

Knowledge Enabled Information and Services Science Diabetes mellitus adversely affects the outcomes in patients with myocardial infarction (MI), due in part to the exacerbation of left ventricular (LV) remodeling. Although angiotensin II type 1 receptor blocker (ARB) has been demonstrated to be effective in the treatment of heart failure, information about the potential benefits of ARB on advanced LV failure associated with diabetes is lacking. To induce diabetes, male mice were injected intraperitoneally with streptozotocin (200 mg/kg). At 2 weeks, anterior MI was created by ligating the left coronary artery. These animals received treatment with olmesartan (0.1 mg/kg/day; n = 50) or vehicle (n = 51) for 4 weeks. Diabetes worsened the survival and exaggerated echocardiographic LV dilatation and dysfunction in MI. Treatment of diabetic MI mice with olmesartan significantly improved the survival rate (42% versus 27%, P < 0.05) without affecting blood glucose, arterial blood pressure, or infarct size. It also attenuated LV dysfunction in diabetic MI. Likewise, olmesartan attenuated myocyte hypertrophy, interstitial fibrosis, and the number of apoptotic cells in the noninfarcted LV from diabetic MI. Post-MI LV remodeling and failure in diabetes were ameliorated by ARB, providing further evidence that angiotensin II plays a pivotal role in the exacerbated heart failure after diabetic MI. ARB causes heart failure Extracting the Relationship Angiotensin II type 1 receptor blocker attenuates exacerbated left ventricular remodeling and failure in diabetes-associated myocardial infarction., Matsusaka H, et. al.

Knowledge Enabled Information and Services Science Scenario 2 Status: Completed research Where: NIH/NIDA What: Understanding the genetic basis of nicotine dependence. How: Semantic Web technologies (especially RDF, OWL, and SPARQL) support information integration and make it easy to create semantic mashups (semantically integrated resources).

Knowledge Enabled Information and Services Science Entrez Gene Reactome KEGG HumanCyc GeneOntology HomoloGene Genome and pathway information integration pathway protein pmid pathway protein pmid pathway protein pmid GO ID HomoloGene ID

Knowledge Enabled Information and Services Science BioPAX ontology Entrez Knowledge Model (EKoM)

Knowledge Enabled Information and Services Science Biological Significance Biological Significance: Understand the role of genes in nicotine addiction Treatment of drug addiction based on genetic factors Identify important genes and use for pharmaceutical productions Gene-Pathway Data Integration– Understanding the Genetic-basis of Nicotine Dependence Collaborators Gene-Pathway Data Integration– Understanding the Genetic-basis of Nicotine Dependence Collaborators: NIDA, NLM

Knowledge Enabled Information and Services Science Scenario 3 Status: Completed research Where: NIH What: queries across integrated data sources –Enriching data with ontologies for integration, querying, and automation –Ontologies beyond vocabularies: the power of relationships

Knowledge Enabled Information and Services Science Use data to test hypothesis gene GO PubMed Gene name OMIM Sequence Interactions Glycosyltransferase Congenital muscular dystrophy Link between glycosyltransferase activity and congenital muscular dystrophy? Adapted from: Olivier Bodenreider, presentation at HCLS Workshop, WWW07

Knowledge Enabled Information and Services Science In a Web pages world… Congenital muscular dystrophy, type 1D (GeneID: 9215) has_associated_disease has_molecular_function Acetylglucosaminyl- transferase activity Adapted from: Olivier Bodenreider, presentation at HCLS Workshop, WWW07

Knowledge Enabled Information and Services Science With the semantically enhanced data MIM: Muscular dystrophy, congenital, type 1D GO: has_associated_phenotype has_molecular_function EG:9215 LARGE acetylglucosaminyl- transferase GO: glycosyltransferase GO: isa GO: acetylglucosaminyl- transferase GO: From medinfo paper. Adapted from: Olivier Bodenreider, presentation at HCLS Workshop, WWW07 SELECT DISTINCT ?t ?g ?d { ?t is_a GO: ?g has molecular function ?t. ?g has_associated_phenotype ?b2. ?b2 has_textual_description ?d. FILTER (?d, “muscular distrophy”, “i”). FILTER (?d, “congenital”, “i”) }

Knowledge Enabled Information and Services Science Scenario 4 Status: Research prototype and in progress Where: UGA What: –Semantic Problem Solving Environment (PSE) for Trypanosoma cruzi (Chagas Disease) Workflow with Semantic Annotation of Experimental Data already in use Knowledge driven query formulation

Knowledge Enabled Information and Services Science Knowledge driven query formulation Complex queries can also include: - on-the-fly Web services execution to retrieve additional data - inference rules to make implicit knowledge explicit

Knowledge Enabled Information and Services Science Scenario 5 When: Research in progress Where: Cincinatti Children’s Hospital Medical Center, AFRL What: scientific literature mining –Dealing with unstructured information –Extracting knowledge from text –Complex entity recognition –Relationship extraction

Knowledge Enabled Information and Services Science Method – Parse Sentences in PubMed SS-Tagger (University of Tokyo) SS-Parser (University of Tokyo) (TOP (S (NP (NP (DT An) (JJ excessive) (ADJP (JJ endogenous) (CC or) (JJ exogenous) ) (NN stimulation) ) (PP (IN by) (NP (NN estrogen) ) ) ) (VP (VBZ induces) (NP (NP (JJ adenomatous) (NN hyperplasia) ) (PP (IN of) (NP (DT the) (NN endometrium) ) ) ) ) ) ) Entities (MeSH terms) in sentences occur in modified forms “adenomatous” modifies “hyperplasia” “An excessive endogenous or exogenous stimulation” modifies “estrogen” Entities can also occur as composites of 2 or more other entities “adenomatous hyperplasia” and “endometrium” occur as “adenomatous hyperplasia of the endometrium”

Knowledge Enabled Information and Services Science What can we do with the extracted knowledge? Semantic browser demo

Knowledge Enabled Information and Services Science Conclusion Semantic web technologies can help with: –Fusion of data: semi-structured, structured, experimental, literature, multimedia –Analysis and mining of data, extraction, annotation, capture provenance of data through annotation, workflows with SWS –Querying of data at different levels of granularity, complex queries, knowledge-driven query interface –Perform inference across data sets

Knowledge Enabled Information and Services Science Researchers: Satya Sahoo, Cartic Ramakrishnan, Pablo Mendes and Kno.e.sis teamKno.e.sis Collaborators: Athens Heart Center (Dr. Agrawal), CCHMC (Bruce Aronow), NLM (Olivier Bodenreider), CCRC-UGA (Will York), UGA (Tarleton), Bioinformatics-WSU (Raymer) Funding: NIH/NCRR, NIH/NLBHI, NSF

Knowledge Enabled Information and Services Science References 1.A. Sheth, S. Agrawal, J. Lathem, N. Oldham, H. Wingate, P. Yadav, and K. Gallagher, Active Semantic Electronic Medical Record, Intl Semantic Web Conference, 2006.Active Semantic Electronic Medical Record, Intl Semantic Web Conference 2.Satya Sahoo, Olivier Bodenreider, Kelly Zeng, and Amit Sheth, An Experiment in Integrating Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information WWW2007 HCLS Workshop, May 2007.An Experiment in Integrating Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information WWW2007 HCLS Workshop 3.Satya S. Sahoo, Kelly Zeng, Olivier Bodenreider, and Amit Sheth, From "Glycosyltransferase to Congenital Muscular Dystrophy: Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology, Amsterdam: IOS, August 2007, PMID: , pp From "Glycosyltransferase to Congenital Muscular Dystrophy: Integrating Knowledge from NCBI Entrez Gene and the Gene Ontology 4.Satya S. Sahoo, Olivier Bodenreider, Joni L. Rutter, Karen J. Skinner, Amit P. Sheth, An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence, submitted, Cartic Ramakrishnan, Krzysztof J. Kochut, and Amit Sheth, "A Framework for Schema-Driven Relationship Discovery from Unstructured Text", Intl Semantic Web Conference, 2006, pp A Framework for Schema-Driven Relationship Discovery from Unstructured Text", Intl Semantic Web Conference 6.Satya S. Sahoo, Christopher Thomas, Amit Sheth, William S. York, and Samir Tartir, "Knowledge Modeling and Its Application in Life Sciences: A Tale of Two Ontologies", 15th International World Wide Web Conference (WWW2006), Edinburgh, Scotland, May 23-26, 2006.Knowledge Modeling and Its Application in Life Sciences: A Tale of Two Ontologies Demos at: